How to Annotate Mendeley PDFs on iPad
What happens to a highlight, a note, or an Apple Pencil stroke after you make it on an iPad — where Mendeley can store it, where it cannot, and why.
You have a paper open on the iPad and you draw a line under a sentence. Where does that line live now?
The answer is not the same for every kind of mark you can make, and it is not the same for every way of getting the paper onto the iPad in the first place. This article works through what Mendeley can store, what it cannot, and what that means for the marks you are about to make.
What Mendeley Stores as an Annotation
Mendeley's own developer documentation defines an annotation as a type plus a place on a page. There are three types:
| Type | What it is | How it is positioned |
|---|---|---|
highlight | A highlighted span | A bounding rectangle: top-left and bottom-right |
sticky_note | A note pinned to a point | The same rectangle with zero dimensions — a point |
note | A comment on the document as a whole | No page position |
An annotation also carries a colour, the profile that made it, and whether it is private or shared with a group. Coordinates are typographic points measured from the lower-left corner of the page.
That is the whole model. It is a good fit for the things people do to text — mark a span, pin a comment to a spot — and it means those marks are structured data rather than pixels burned into a file. It also has a consequence that matters on an iPad, which the rest of this article is about.
If You Annotate in the Browser
Mendeley's web interface lets you highlight and add notes, and those go straight into your library as annotations of the types above. Nothing is stranded: what you do on the web is there on the desktop.
The limits are the browser's. There is no pressure-sensitive input, no palm rejection, and the page is a page — you are working at whatever size the screen gives you.
If You Annotate in a Separate PDF App
Download the PDF, open it in a reader, mark it up there. This is the route with the best annotation tools, and it is the route where your marks leave your library.
The annotations you make belong to that copy of the file, in that app. Mendeley has no idea they happened. The catalogued paper and the annotated paper are now two different objects, and the one your citation points at is not the one you wrote on. Months later this is genuinely hard to untangle — which is why it is worth deciding early rather than discovering it in a literature review.
Some readers can export annotations back out as a flattened PDF or a summary. That helps, but a flattened annotation is no longer structured data: it cannot be searched, filtered by colour, or edited in Mendeley the way a native highlight can.
If You Annotate in an App That Syncs
An app that signs in to your Mendeley account can create annotations through the same API the web interface uses. A highlight made on the iPad becomes a highlight in your library, at the same coordinates, in the same colour — and a highlight made on the desktop last month is there when you open the paper on the iPad.
This is the only route where there is one copy of the paper rather than two.
What varies between apps in this category is which of your marks make that trip. Which brings us to the one that does not.
Why Handwriting Is Different
Look at the model again: a type, and a rectangle on a page.
A handwritten stroke is not a rectangle. It is a path — a sequence of points, with pressure and tilt and a width that changes along its length. There is no field in Mendeley's annotation model that can hold one. This is not an app failing to implement something; it is a shape that the format does not have a slot for.
So no app can turn your Apple Pencil handwriting into a Mendeley annotation. Anything that claims to is doing something else — flattening the ink into the PDF as pixels, or storing it somewhere outside Mendeley and showing it back to you.
The second of those is the honest version, and it is worth knowing which an app does, because the two behave very differently when you open the paper somewhere else.
Offline, and When Two Devices Disagree
Two more things decide how annotation feels over a semester.
Offline. Marks made without a connection have to be held locally and sent when there is one. An app that only writes through the API at the moment you draw will lose work on a plane.
Conflicts. Two devices, both with your library, both edited. Or a sync that would remove more annotations than it should. Annotation is not the kind of data where the newer copy should silently win — a semester of margin notes has no undo. It is worth knowing whether an app resolves this quietly or stops and tells you.
Where Rectoly Fits
Rectoly creates real Mendeley annotations. Highlights, underlines and sticky notes made on the iPad appear in your library as annotations, and annotations made elsewhere are there when you open the paper. One copy, both directions.
Handwriting takes the honest version of the second route above. Because Mendeley has no ink type, Apple Pencil strokes are kept outside the annotation model: they travel between your own Apple devices through iCloud, and — unless you turn it off — are stored on the Mendeley item as an attached file, so they are not tied to one iPad. What they do not do is appear drawn on the page inside Mendeley itself, because there is nothing there to draw them with.
Marks made offline are stored on the device and go up when you reconnect. If a sync round would erase most of a paper's handwriting, or two devices disagree, Rectoly stops and tells you rather than resolving it quietly.
Frequently Asked Questions
Can I highlight a Mendeley PDF on an iPad and see it on my computer?
Yes, if you use an app that creates annotations through your Mendeley account. Highlights, underlines and sticky notes are exactly the types Mendeley stores, so they appear on the desktop like any other annotation.
Why does my Apple Pencil handwriting not show up in Mendeley?
Mendeley's annotation model covers highlights, sticky notes and notes, each positioned by a rectangle on a page. A handwritten stroke is a path, not a rectangle, so there is no way to store one as a Mendeley annotation. Apps that keep your handwriting are storing it outside that model.
If I annotate a downloaded PDF in another reader, can I get those marks into Mendeley?
Not as annotations. You can usually export a flattened copy with the marks burned in and attach that to the item, but the result is an image of your annotations rather than annotations Mendeley can search or edit.
Do my existing Mendeley annotations show up on the iPad?
With an app that syncs, yes — annotations are read as well as written, so what you marked on the desktop is there when you open the paper.
Conclusion
Before you commit a semester of reading to a workflow, it is worth knowing which of your marks are structured data in your library and which are pixels in a file somewhere.
Highlights, underlines and sticky notes can be the former. Handwriting cannot — not because of any one app, but because the format has no shape for it. What an app can do is keep your handwriting somewhere sensible and tell you honestly where that is.